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Positive Selection and Climatic Effects on MHC Class II Gene Diversity In www.nature.com/scientificreports OPEN Positive selection and climatic efects on MHC class II gene diversity in hares (Lepus capensis) Received: 21 December 2017 Accepted: 16 July 2018 from a steep ecological gradient Published: xx xx xxxx Asma Awadi1, Hichem Ben Slimen1,2, Steve Smith 3, Felix Knauer3, Mohamed Makni1 & Franz Suchentrunk3 In natural populations, allelic diversity of the major histocompatibility complex (MHC) is commonly interpreted as resulting from positive selection in varying spatiotemporal pathogenic landscapes. Composite pathogenic landscape data are, however, rarely available. We studied the spatial distribution of allelic diversity at two MHC class II loci (DQA, DQB) in hares, Lepus capensis, along a steep ecological gradient in North Africa and tested the role of climatic parameters for the spatial distribution of DQA and DQB proteins. Climatic parameters were considered to refect to some extent pathogenic landscape variation. We investigated historical and contemporary forces that have shaped the variability at both genes, and tested for diferential selective pressure across the ecological gradient by comparing allelic variation at MHC and neutral loci. We found positive selection on both MHC loci and signifcantly decreasing diversity from North to South Tunisia. Our multinomial linear models revealed signifcant efects of geographical positions that were correlated with mean annual temperature and precipitation on the occurrence of protein variants, but no efects of co-occurring DQA or DQB proteins, respectively. Diversifying selection, recombination, adaptation to local pathogenic landscapes (supposedly refected by climate parameters) and neutral demographic processes have shaped the observed MHC diversity and diferentiation patterns. Genetic studies of natural populations based on presumably neutral markers such as mitochondrial d-loop DNA (mtDNA), microsatellites or SNPs are important to infer phylogeny, population history and gene fow1,2. However, in some cases the time span between the separation of populations might be too short or gene fow might be too strong to leave a signal of diferentiation at neutral loci3. In such cases, diferences between populations can only be detectable at functional genes under selection3. Moreover, studying molecular polymorphism at loci under natural selection will help to understand the genetics of adaptive processes and to increase our knowledge on the importance of adaptive genetic variability in free ranging animal populations1. Local adaptation at functional markers has mainly been addressed in populations structured at neutral markers and rarely in the case of seem- ingly panmictic populations4. A study of Tunisian hare populations indicated a strong population structure at mitochondrial OXPHOS genes, which are under positive selection at several codons, despite a high gene fow at neutral markers5. Tese fndings are consistent with local adaptation according to climate variation5. Adaptation to local or regional pathogenic landscapes is ofen addressed by analyses of major histocompatibil- ity genes (MHC) which code for glycoproteins that recognize and bind antigens in order to present them to CD4+ and CD8+T-lymphocytes to initiate the adaptive immune response against pathogens. MHC class I and class II loci, the two main types of MHC loci involved in the adaptive immune system, have been shown to be highly pol- ymorphic in a wide range of species6–9 and their adaptive signifcance in vertebrates has long been recognized10,11. Allelic diversity at these loci can be associated with variation across environmental and geographical scales as demonstrated from several studies12,13. Te role of environmental characteristics in shaping selective pressures 1Unité de Recherche Génomique des Insectes Ravageurs des Cultures d’Intérêt Agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia. 2Institut Supérieur de Biotechnologie de Béja, University of Jendouba, Avenue Habib Bourguiba Béja 9000, BP. 382, Béja, Tunisia. 3Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria. Correspondence and requests for materials should be addressed to A.A. (email: [email protected]) SCIENTIFIC REPORTS | (2018) 8:11514 | DOI:10.1038/s41598-018-29657-3 1 www.nature.com/scientificreports/ on MHC genes is suggested to be mediated by combined efects including recent and ancient demography as well as behavioural and ecological diferences in pathogens exposure14–16. Moreover, host-pathogen interactions have been suggested to be afected by temperature, nutrient availability and environmental stress17. Whereas increases of ambient temperature can reinforce selection on immune genes, thereby accelerating host adaptation18,19, vari- ation in nutrient levels can force physiological modifcation that could either impair or promote local adaptation of the host17. Among all MHC molecules, class II genes have received the most attention, due to their role in studying mech- anisms and signifcance of molecular adaptation in vertebrates20 and host parasite co-evolution2. MHCII mole- cules are heterodimers formed by an α and a β chain encoded by A and B genes, respectively21,22. Tese chains are characterized by several typical structures, such as N-linked glycosylation sites, connecting peptides, transmem- brane regions, and cytoplasmic domains, as well as the α1/α2 domain and the β1/β2 domain, respectively23. Te α1 and β1 domains constitute the peptide-binding region (PBR), involved with the recognition and binding to the antigens14,24,25. Tese domains are highly polymorphic and are encoded by the second exon of A and B MHCII genes. Given their role in presenting antigenic determinant peptides to the cell surface, these loci are typically expected to be subject to strong positive selection, since their greater allelic diversity should be associated with a response to a wider range of pathogens16. Genetic diversity in the MHC is also generated through several mecha- nisms, including point mutation, recombination, gene conversion, sexual selection and maternal–foetal interac- tions25–28. Te variation generated by these processes is thought to be maintained in individuals and populations by a combination of balancing and diversifying selection, driven primarily by variation in selection pressure from pathogens and parasites across space and time3,28. Balancing selection encompasses a number of diferent evolutionary mechanisms that result in a large number of alleles being maintained in populations for longer than would be expected relative to neutral genetic variation24. Such balancing selection is generally explained by three mechanisms a) over-dominant selection or heterozygote advantage where heterozygous individuals have higher ftness than both corresponding homozygotes; b) frequency dependent selection or rare allele advantage where individuals with rare genotypes have higher ftness29,30; c) fuctuation in selection pressure where MHC polymor- phism is maintained by changing pathogen composition through time and space. Conversely, under diversifying selection at MHC loci, the spread of an advantageous allele (positive selection) would be expected to lead to a loss of genetic variation. Similarly, selection against disadvantageous alleles (negative or purifying selection) would also be expected to reduce diversity31. Among the diferent suggested mechanisms of balancing selection, fuctua- tion in selection pressure have been reported for class II MHC genes among populations of the Asian cygomolgus macaque (Macaca fascicularis)12, and the Atlantic salmon32, among other studies. Patterns of MHC selection can be inferred by comparing MHC genetic diferentiation to diferentiation at presumably neutral markers28. Neutral loci refect demographic factors such as migration and drif, whereas loci under selection usually show higher diferentiation under diferent local selection regimes or lower diferentiation under balancing selection28,33 or under negative/purifying selection33. Higher diferentiation at MHC genes could therefore refect local adaptation to diferent parasite faunas prevailing in the respective populations. In Tunisia, hares (Lepus capensis) are distributed throughout the whole country in diverse environments and over short geographic distances, reaching from the Mediterranean climate in the north to the pronounced arid desert climate (Sahara) in the south. Tis situation provides a good precondition to study natural selection and adaptation on functional genes5. Te likely diferences in diferential parasite pressure in these habitats could lead to diferent selection pressure at MHC loci among the local populations. Such selective pressure would shape diversity and diferentiation profles in interaction with neutral demographic/stochastic factors. In this study, we examined the MHC class II polymorphism for DQA and DQB genes in hares from Tunisia along a steep ecological gradient. We frst investigated the variation of genetic diversity in the diferent studied populations distributed in heterogeneous ecoregions from North to South. If diversifying selection is the main evolutionary force acting on MHC genes, we expected signifcant genetic diferentiation despite observed high gene fow in neutral markers. Second, we used diferent approaches to evaluate the efect of selective pressure in each codon of the obtained sequences. Moreover, we compared the levels of allelic diversity of the considered hare
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